Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AZOBR_RS08240 AZOBR_RS08240 ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__azobra:AZOBR_RS08240 Length = 505 Score = 246 bits (629), Expect = 7e-70 Identities = 147/325 (45%), Positives = 191/325 (58%), Gaps = 45/325 (13%) Query: 32 IADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASPHLADNFAAFAAMFP 91 I L L Y++L GLNIVVG AGLLDLGYVAFYAVGAY +AL+A ++ F Sbjct: 175 IGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLA------HYFGF----- 223 Query: 92 NGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVN 151 S W+ +P+A LAA G +LG P L+LRGDY AIVTLGFGEIIRI L N Sbjct: 224 -----SFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILINW---YQ 275 Query: 152 LTNGPKGLGQIDSVKVFGLDLGKRL---------EVFGFD---INSVTLYYYLFLVLVVV 199 T GP G+ I FG+ R E+FG + ++ + YYL LVL +V Sbjct: 276 FTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILVLALV 335 Query: 200 SVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQ 259 + R++ +GRAW A+RED+IA ++GIN NMKL AF + A FGG +G+ F Q Sbjct: 336 VNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFATRQ 395 Query: 260 GFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDGRL 319 GF+SPESF+ +ES +I+A+VVLGG+G GV++ A L+ LPE R +A Sbjct: 396 GFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELAD---------- 445 Query: 320 DSAILRQLLIALAMIIIMLLRPRGL 344 R L + M++IML RPRGL Sbjct: 446 ----YRMLAFGMGMVLIMLWRPRGL 466 Lambda K H 0.328 0.144 0.430 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 469 Number of extensions: 25 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 358 Length of database: 505 Length adjustment: 32 Effective length of query: 326 Effective length of database: 473 Effective search space: 154198 Effective search space used: 154198 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory